Single-Round DNA Aptamer Selection by Combined Use of Capillary Electrophoresis and Next Generation Sequencing: An Aptaomics Approach for Identifying Unique Functional Protein-Binding DNA Aptamers

In DNA aptamer selection, existing methods do not discriminate aptamer sequences based on their binding affinity and function and the reproducibility of the selection is often poor, even for the selection of well-known aptamers like those that bind the commonly used model protein thrombin. In the present study, a novel single-round selection method (SR-CE selection) was developed by combining capillary electrophoresis (CE) with next generation sequencing. Using SR-CE selection, a successful semi-quantitative and semi-comprehensive aptamer selection for thrombin was demonstrated with high reproducibility for the first time. Selection rules based on dissociation equilibria and kinetics were devised to obtain families of analogous sequences. Selected sequences of the same family were shown to bind thrombin with high affinity. Furthermore, data acquired from SR-CE selection was mined by creating sub-libraries that were categorized by the functionality of the aptamers (e. g., pre-organized aptamers versus structure-induced aptamers). Using this approach, a novel fluorescent molecular recognition sensor for thrombin with nanomolar detection limits was discovered. Thus, in this proof-of-concept report, we have demonstrated the potential of a “DNA Aptaomics” approach to systematically design functional aptamers as well as to obtain high affinity aptamers.     

Effect of adsorbed water on the electrorheology of silica suspensions

Monodisperse silica particles were formed by hydrolyzing tetraethylorthosilicate in an ethanol solution and the silica suspensions dispersed in a silicone oil were prepared by a different procedure. The effects of adsorbed water on the electrorheological (ER) behavior were studied under oscillatory shear. The amounts of adsorbed water and surface silanol groups were determined by thermogravimetric analysis. The magnitude of the complex viscosity, |η^*|, increases with the application of electric fields. The physically adsorbed water is primarily responsible for the ER effect. However, the fluids containing large amounts of adsorbed water do not always show excellent ER performance. The surface silanol groups have an important role in promoting the ER effect. Not only the amount but also the situation of silanol groups determines the ER activity of adsorbed water.     

Cationic ring-opening transfer polymerization of spiro ortho esters initiated by carbon black

The ring-opening transfer polymerization of spiro ortho esters (SOE) initiated by carbon black was investigated. In the absence of carbon black, no polymerization occurred at all. In the presence of channel black containing carboxyl group, the ring-opening transfer polymerization of SOE was initiated at 50-70°C. to give polyether ester, namely alternating copolymer of epoxide and lactone. The rate of polymerization of 1,4,6-trioxaspiro[4.4]nonane and 1,4,6-trioxaspiro[4.5]decane was considerably small compared with that of 1,4,6-trioxaspiro[4.6]undecane. The activation energy of the polymerization of 2-chloromethyl-1,4,6-trioxaspiro[4.6]undecane was estimated to be 6.0 kcal/mol. The initiating activity of carbon black increased with an increase in carboxyl group content of carbon black. Furnace black that contained no carboxyl group was unable to initiate the polymerization. Furthermore, the carbon black lost the initiating ability of the polymerization upon the blocking of carboxyl group on the surface by the treatment with potassium hydroxide or diazomethane. Based on these results, it was concluded that carboxyl group on carbon black plays an important role in the initiation. During the polymerization, a part of the polymer formed was grafted onto carbon black: the grafting ratio was 10–30%. The mechanisms of initiation and grafting were discussed.     

Kinetics of hydrogen abstraction reaction between trifluoromethyl formate and OH radical: A theoretical investigation

Kinetics and mechanism of the hydrogen abstraction reaction between trifluoromethyl formate, CF₃OCHO, and OH radical have been investigated by using ab initio molecular orbital theory up to G2(MP2) level. The hydrogen abstraction rate constant has been calculated for the first time over a temperature range of 250–450 K by using standard transition state theory including the tunneling correction. Arrhenius parameters of the reaction have been estimated from the temperature dependence of the calculated rate constant. The calculated value for the rate constant (2.0 × 10^?14 cm³ molecule^?1 s^?1) at 298 K is found to be in very good agreement with the recent experimental results. © 2002 Wiley Periodicals, Inc. Int J Chem Kinet 34: 500–507, 2002     

Asymmetric synthesis of bicyclo[n.1.0]alkanes by the enantioselective 1,3-CH insertion reaction of chiral magnesium carbenoids

Treatment of enantiomerically pure 1-chlorovinyl p-tolyl sulfoxides, derived from cyclic ketones and (R)-chloromethyl p-tolyl sulfoxide, with the lithium enolate of tert-butyl carboxylates gave adducts in quantitative yields as single diastereomers. The adducts were treated with i-PrMgCl in toluene to afford optically active bicyclo[n.1.0]alkanes bearing a tert-butyl carboxylate moiety in up to 99% enantiomeric excess through the enantioselective 1,3-CH insertion reaction of the generated chiral magnesium carbenoids. This is the first example of the enantioselective 1,3-CH insertion reaction of magnesium carbenoid.     

Integrated squared error of kernel-type estimator of distribution function

Let X ₁ ,...,X _n be a random sample drawn from distribution function F(x) with density function f(x) and suppose we want to estimate X(x). It is already shown that kernel estimator of F(x) is better than usual empirical distribution function in the sense of mean integrated squared error. In this paper we derive integrated squared error of kernel estimator and compare the error with that of the empirical distribution function. It is shown that the superiority of kernel estimators is not necessarily true in the sense of integrated squared error.     

Observation of the Fano-Kondo antiresonance in a quantum wire with a side-coupled quantum dot

We have observed the Fano-Kondo antiresonance in a quantum wire with a side-coupled quantum dot. In a weak coupling regime, dips due to the Fano effect appeared. As the coupling strength increased, conductance in the regions between the dips decreased alternately. From the temperature dependence and the response to the magnetic field, we conclude that the conductance reduction is due to the Fano-Kondo antiresonance. At a Kondo valley with the Fano parameter q approximately 0, the phase shift is locked to pi/2 against the gate voltage when the system is close to the unitary limit in agreement with theoretical predictions by Gerland et al. [Phys. Rev. Lett. 84, 3710 (2000)].     

Observation of "partial coherence" in an Aharonov-Bohm interferometer with a quantum dot

We report experiments on the interference through spin states of electrons in a quantum dot (QD) embedded in an Aharonov-Bohm (AB) interferometer. We have picked up a spin-pair state, for which the environmental conditions are ideally similar. The AB amplitude is traced in a range of gate voltage that covers the pair. The behavior of the asymmetry in the amplitude around the two Coulomb peaks agrees with the theoretical prediction that the spin-flip process in a QD is related to the quantum dephasing of electrons. These results constitute evidence of "partial coherence" due to an entanglement of spins in the QD and in the interferometer.